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Molecular beam epitaxy takes place in high vacuum or ultra-high vacuum (10−8Pa). The most important aspect of MBE is the deposition rate (typically less than 3000 nm per hour) allows the films to grow epitaxially. These deposition rates require proportionally better vacuum to achieve the same impurity levels as other deposition techniques. The absence of carrier gases as well as the ultra high vacuum environment result in the highest achievable purity of the grown films.

In solid-source MBE, elements such as gallium and arsenic, in ultra-pure form, are heated in separate quasi-Knudsen effusion cells until they begin to slowly sublime. The gaseous elements then condense on the wafer, where they may react with each other. In the example of gallium and arsenic, single-crystal gallium arsenide is formed. The term "beam" means that evaporated atoms do not interact with each other or vacuum chamber gases until they reach the wafer, due to the long mean free paths of the atoms.

In systems where the substrate needs to be cooled, the ultra-high vacuum environment within the growth chamber is maintained by a system of cryopumps, and cryopanels, chilled using liquid nitrogen or cold nitrogen gas to a temperature close to 77 Kelvin (−196 degrees Celsius). Cryogenic temperatures act as a sink for impurities in the vacuum, so vacuum levels need to be several orders of magnitude better to deposit films under these conditions. In other systems, the wafers on which the crystals are grown may be mounted on a rotating platter which can be heated to several hundred degrees Celsius during operation.

Lately molecular beam epitaxy has been used to deposit oxide materials for advanced electronic, magnetic and optical applications. For these purposes, MBE systems have to be modified to incorporate oxygen sources.[2]

The ATG (Asaro-Tiller-Grinfeld) instability, also known as the Grinfeld instability, is an elastic instability often encountered during molecular beam epitaxy. If there is a mismatch between the lattice sizes of the growing film and the supporting crystal, elastic energy will be accumulated in the growing film. At some critical height, the free energy of the film can be lowered if the film breaks into isolated islands, where the tension can be relaxed laterally. The critical height depends on Young's moduli, mismatch size, and surface tensions.